Descriptor File Format

abhb: 10-12 hydrogen bond energy term

This is an outdated form of a specific hydrogen bonding term. (Hydrogen bonding can be properly modeled with a combination of electrostatics and van der Waals terms.)

The abhb term is the sum of Nabhb terms, each of the form:


H[ rinclude - rij ] { A / rij12 - B / rij10 }

where rij is the distance between the atoms atomi and atomj, A and B are constants and H[r] is the Heaviside step function in which H[r<0] = 1, H[r=0] = 1/2 and H[r>0] = 0. The function is abruptly terminated at rinclude. The abhb record in the descriptor has the form

abhb
Npair
rinclude
rcutoff

atomi
A
B
Nij

atomij
...

...
...
...
...

The abhb record starts with the keyword abhb followed by the number of pair lists Npair, the distance at which the function will be terminated rinclude and the cutoff distance rcutoff, followed by Npair lists. Each list starts with an atom number atomi, followed by the parameters A and B and the number of atoms that interact with atomi with these parameters Nij and finally the Nij atom numbers atomij, ... The sum of all the values of Nij equals Nabhb. rcutoff has to be larger than rinclude. The calculation of the abhb term is done for a subset of the full list, from a candidate list. The candidate list contains atom pairs that are within a distance rcutoff apart. This list is updated regularly. In between updates, some of the atom pairs in the candidate list move apart, while pairs of atoms that are not in the candidate list move closer together. The distance rcutoff and the list update interval are chosen to reduce computation by reducing the difference between rinclude and rcutoff and by increasing the interval between list updates. These are mutually incompatible. Example:


abhb 2 9.0 12.0
3   8561000   2568000   3
    45  15  57
4   62290000   11960000   2
    15  35

There are two inclusion lists, the first has three pairs involving atom 3, the second has two pairs involving atom 4. The first set of hydrogen bond has the energy minimum at 2Å while the second minimum is at 2.5Å. rinclude is 9Å which is perhaps inadequate given the positions of the minima.


Details of Descriptor Records
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tors
itor
iton
nbn+
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ele+
ele-
vdw+
vdw-
abhb
noen
surf
stud
vlat
boun
lock

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